qdiv 4.0.5

Microbial diversity analysis toolkit

qdiv: Microbial Diversity Analysis Toolkit

qdiv is a Python toolkit for microbial diversity analysis, built around the robust and intuitive Hill number framework.

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Features

• Data Management: Load and validate data from multiple formats (CSV/TSV, FASTA, Newick). Functions for subsetting, rarefaction, merging, renaming, tree pruning, and more.

• Diversity analysis: Compute multiple alpha and beta diversity metrics based on the Hill number framework.

• Statistical methods: Integrate diversity metrics using the Hill number framework into null models (Raup–Crick, NRI, NTI), ordinations (PCoA, db-RDA), PERMANOVA, and Mantel tests.

• Visualization: Heatmaps, ordinations, and diversity plots, and more.

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Installation

pip install qdiv

Optional acceleration (Numba)

Some functions in the sequence_comparisons module support compilation via Numba. Installing qdiv with the optional accelerate extra enables faster sequence distance computations.

pip install qdiv[accelerate]

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Documentation

Full documentation is available at: https://qdiv.readthedocs.io

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Licence

From version 4.0.0, qdiv is licensed under the https://opensource.org/licenses/BSD-3-Clause. Previous versions were released under the GNU General Public License v3.0 (GPL-3.0).

Contributing

Contributions are welcome! Please read the CONTRIBUTING.md for details on:

• How to report bugs
• How to request new features
• How to submit pull requests

Support

If you need help with qdiv:

• Browse existing issues
• If needed, open a support issue. See SUPPORT.md.

Code of Conduct

To ensure a welcoming environment, this project follows the standards outlined in the CODE_OF_CONDUCT.md. All contributors are expected to uphold this code.

Citation

If you use qdiv in your research, please cite:

Modin. (2026). qdiv: A Python package for microbial ecology analysis using the Hill number framework. Journal of Open Source Software, 11(121), 10089. https://doi.org/10.21105/joss.10089.

Download the citation here:

CITATION.cff